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Climate is a crucial driver of the distributions and activity of multiple biotic and abiotic processes, and thus high-quality and high-resolution climate data are often prerequisite in various environmental research. However, contemporary gridded climate products suffer critical problems mainly related to sub-optimal pixel size and lack of local topography-driven temperature heterogeneity. Here, by integrating meteorological station data, high-quality terrain information and multivariate modelling, we aim to explicitly demonstrate this deficiency. Monthly average temperatures (1981-2010) from Finland, Sweden and Norway were modelled using generalized additive modelling under (1) a conventional (i.e. considering geographical location, elevation and water cover) and (2) a topoclimatic framework (i.e. also accounting for solar radiation and cold-air pooling). The performance of the topoclimatic model was significantly higher than the conventional approach for most months, with bootstrapped mean R-2 for the topoclimatic model varying from 0.88 (January) to 0.95 (October). The estimated effect of solar radiation was evident during summer, while cold air pooling was identified to improve local temperature estimates in winter. The topoclimatic modelling exposed a substantial temperature heterogeneity within coarser landscape units (>5 degrees C/1 km(-2) in summer) thus unveiling a wide range of potential microclimatic conditions neglected by the conventional approach. Moreover, the topoclimatic model predictions revealed a pronounced asymmetry in average temperature conditions, causing isotherms during summer to differ several hundreds of metres in altitude between the equator and pole facing slopes. In contrast, cold-air pooling in sheltered landscapes lowered the winter temperatures ca. 1.1 degrees C/100m towards the local minimum altitude. Noteworthy, the analysis implies that conventional models produce biassed predictions of long-term average temperature conditions, with errors likely to be high at sites associated with complex topography.

The olive fruit fly (OFF), Bactrocera oleae is the most devastating pest affecting olive fruit worldwide. Previous investigations have addressed the fungal microbiome associated with olive drupes or B. oleae, but the impact of the insect on fungal communities of olive fruit remains undescribed. In the present work, the fungal microbiome of olive drupes, infested and non-infested by the OFF, was investigated in four different localities and cultivars. Olive fruit fly infestations caused a general reduction of the fungal diversity, a higher quantity of the total DNA and an increase in taxa that remained unidentified or had unknown roles. The infestations led to imbalanced fungal communities with the growth of taxa that are usually outcompeted. While it was difficult to establish a cause-effect link between fly infestation and specific fungi, it is clear that the fly alters the natural microbial balance, especially the low abundant taxa. On the other hand, the most abundant ones, were not significantly influenced by the insect. In fact, despite the slight variation between the sampling locations, Aureobasidium, Cladosporium, and Alternaria, were the dominant genera, suggesting the existence of a typical olive fungal microbiome.

A long-standing debate concerns whether nectar sugar composition evolves as an adaptation to pollinator dietary requirements or whether it is 'phylogenetically constrained'. Here, we use a modelling approach to evaluate the hypothesis that nectar sucrose proportion (NSP) is an adaptation to pollinators. We analyse similar to 2100 species of asterids, spanning several plant families and pollinator groups (PGs), and show that the hypothesis of adaptation cannot be rejected: NSP evolves towards two optimal values, high NSP for specialist-pollinated and low NSP for generalist-pollinated plants. However, the inferred adaptive process is weak, suggesting that adaptation to PG only provides a partial explanation for how nectar evolves. Additional factors are therefore needed to fully explain nectar evolution, and we suggest that future studies might incorporate floral shape and size and the abiotic environment into the analytical framework. Further, we show that NSP and PG evolution are correlated - in a manner dictated by pollinator behaviour. This contrasts with the view that a plant necessarily has to adapt its nectar composition to ensure pollination but rather suggests that pollinators adapt their foraging behaviour or dietary requirements to the nectar sugar composition presented by the plants. Finally, we document unexpectedly sucrose-poor nectar in some specialized nectarivorous bird-pollinated plants from the Old World, which might represent an overlooked form of pollinator deception. Thus, our broad study provides several new insights into how nectar evolves and we conclude by discussing why maintaining the conceptual dichotomy between adaptation and constraint might be unhelpful for advancing this field.

We investigated the role of N2-fixation by the colony-forming cyanobacterium, Aphanizomenon spp., for the plankton community and N-budget of the N-limited Baltic Sea during summer by using stable isotope tracers combined with novel secondary ion mass spectrometry, conventional mass spectrometry and nutrient analysis. When incubated with 15N2, Aphanizomenon spp. showed a strong 15N-enrichment implying substantial 15N2-fixation. Intriguingly, Aphanizomenon did not assimilate tracers of 15NH4+ from the surrounding water. These findings are in line with model calculations that confirmed a negligible N-source by diffusion-limited NH4+ fluxes to Aphanizomenon colonies at low bulk concentrations (<250 nm) as compared with N2-fixation within colonies. No N2-fixation was detected in autotrophic microorganisms <5 μm, which relied on NH4+uptake from the surrounding water. Aphanizomenon released about 50% of its newly fixed N2 as NH4+. However, NH4+ did not accumulate in the water but was transferred to heterotrophic and autotrophic microorganisms as well as to diatoms (Chaetoceros sp.) and copepods with a turnover time of ~5 h. We provide direct quantitative evidence that colony-formingAphanizomenon releases about half of its recently fixed N2 as NH4+, which is transferred to the prokaryotic and eukaryotic plankton forming the basis of the food web in the plankton community. Transfer of newly fixed nitrogen to diatoms and copepods furthermore implies a fast export to shallow sediments via fast-sinking fecal pellets and aggregates. Hence, N2-fixing colony-forming cyanobacteria can have profound impact on ecosystem productivity and biogeochemical processes at shorter time scales (hours to days) than previously thought.

Experience can help animals adapt their behaviour to fit the environment or conditions that they find themselves in. Understanding how and when experience affects behaviour is important for the animals we rear in captivity. This is particularly true when we rear animals with the intent of releasing them into the wild as part of population rehabilitation and conservation efforts. We investigated how exposure to a changing, more complex environment promotes behavioural development in juvenile trout. Four groups of fish were compared; (i) fish that were maintained without enrichment, (ii) fish that were exposed to an early period of enrichment, but were then returned to a plain environment, (iii) fish that were maintained in plain conditions, but were then exposed to enrichment towards the end of the rearing phase, (iv) a group that were kept in enriched conditions throughout the 12 week rearing period. We then assessed fish anxiety levels, their spatial learning ability, and the capacity of the fish to find their way through a barrier where different routes were presented across 4 different trials. Fish that experienced enriched conditions for the longest duration had superior spatial learning abilities, and they were better at finding the correct route to get past the barrier than fish from the remaining three treatments. Positive effects on behaviour were, however, also found in the fish that only experienced enrichment in the last part of the rearing period, compared to the control, or fish exposed to early enrichment. No effect of enrichment was found on levels of anxiety in any of the groups.

The Lateglacial/early Holocene sediments from the ancient lake at Hasseldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hasseldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerod and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog.

Nutrient load reductions are needed to improve the state of the Baltic Sea, but it is still under debate how they should be implemented. In this paper, we use data from an environmental valuation study conducted in all nine Baltic Sea states to investigate public preferences of relevance to three of the involved decision-dimensions: First, the roles of nitrogen versus phosphorus reductions causing different eutrophication effects; second, the role of time the - lag between actions to reduce nutrient loads and perceived improvements; and third; the spatial dimension and the roles of actions targeting the coastal and open sea environment and different sub-basins. Our findings indicate that respondents view and value the Baltic Sea environment as a whole, and are not focussed only on their local sea area, or a particular aspect of water quality. We argue that public preferences concerning these three perspectives should be one of the factors guiding marine policy. This requires considering the entire range of eutrophication effects, in coastal and open sea areas, and including long-term and short-term measures.

Cyanobacteria are widely distributed primary producers with significant implications for the global biogeochemical cycles of carbon and nitrogen. Diazotrophic cyanobacteria of subsection V (Order Stigonematales) are particularly ubiquitous in photoautotrophic microbial mats of hot springs. The Stigonematal cyanobacterium strain CHPI isolated from the Porcelana hot spring (Chile) was one of the major contributors of the new nitrogen through nitrogen fixation. Further morphological and genetic characterization verified that the strain CHP1 belongs to Stigonematales, and it formed a separate Glade together with other thermophiles of the genera Fischerella and Mastigocladus. Strain CHP1 fixed maximum N-2 in the light, independent of the temperature range. At 50 degrees C niJH gene transcripts showed high expression during the light period, whereas the nifH gene expression at 45 degrees C was arrhythmic. The strain displayed a high affinity for nitrate and a low tolerance for high ammonium concentrations, whereas the narB and glnA genes showed higher expression in light and at the beginning of the dark phase. It is proposed that Mastigocladus sp. strain CHPI would represent a good model for the study of subsection V thermophilic cyanobacteria, and for understanding the adaptations of these photoautotrophic organisms inhabiting microbial mats in hot springs globally.

This paper reviews the most recent progress in exploring silicon-mediated resistance to herbivorous insects and the mechanisms involved. The aim is to determine whether any mechanism seems more common than the others as well as whether the mechanisms are more pronounced in silicon-accumulating than non-silicon-accumulating species or in monocots than eudicots. Two types of mechanisms counter insect pest attacks: physical or mechanical barriers and biochemical/molecular mechanisms (in which Si can upregulate and prime plant defence pathways against insects). Although most studies have examined high Si accumulators, both accumulators and non-accumulators of silicon as well as monocots and eudicots display similar Si defence mechanisms against insects.

Water transparency is one of the ecological indicators for describing water quality and the underwater light field which determines its productivity. In the European Water Framework Directive (WFD) as well as in the European Marine Strategy Framework Directive (MSFD) water transparency is used for ecological status classification of inland, coastal and open sea waters and it is regarded as an indicator for eutrophication in Baltic Sea management (HELCOM, 2007). We developed and compared different empirical and semi-analytical algorithms for lakes and coastal Nordic waters to retrieve Secchi depth (Z(SD)) from remote sensing data (MERIS, 300 m resolution).The algorithms were developed in water bodies with high coloured dissolved organic matter absorption (a(CNOM)(442) ranging 1.7-4.0 m(-1)), Chl a concentration (0.5-73 mg m(-3)) and total suspended matter (0.7-37.5 g m(-3)) and validated against an independent data set over inland and coastal waters (0.6 m < Z(SD) < 14.8 m). The results indicate that for empirical algorithms, using longer wavelengths in the visible spectrum as a reference band decreases the RMSE and increases the coefficient of determination (R-2). The accuracy increased (R-2 = 0.75, RMSE = 1.33 m, n = 134) when Z(SD) was retrieved via an empirical relationship between Z(SD) and K-d (490). The best agreement with in situ data was attained when Z(SD) was calculated via both the diffuse and the beam attenuation coefficient (R-2 = 0.89, RMSE = 0.77 m, n = 89). The results demonstrate that transparency can be retrieved with high accuracy over various optical water types by the means of ocean color remote sensing, improving both the spatial and temporal coverage. The satellite derived Z(SD) product could be therefore used as an additional source of information for WFD and MSFD reporting purposes.

In this study, empirical and semianalytical algorithms are developed and compared for optically complex waters to retrieve the diffuse attenuation coefficient of downwelling irradiance (Kd(lambda)) from satellite data. In the first approach, a band ratio algorithm was used. Various sets of MERIS band ratios were tested to achieve the best estimates for K-d(490) based on the in situ dataset which was measured in Nordic lakes (oligotrophic to eutrophic conditions). In the second approach, K-d(490) was expressed as a function of inherent optical properties which were retrieved from MERIS standard products. The algorithms from both approaches were tested against an independent data set and validated in optically complex coastal waters in the Baltic Sea and in Nordic lakes with high concentrations of coloured dissolved organic matter (0.3 < a(cdom)(442) m(-1) < 4.5), chlorophyll a (Chl a) (0.7< C-Chl a(mg m(-3))< 67.5) and total suspended matter (TSM) (0.5 < C-TSM(g m(-3)) < 26.4). MERIS-derived K-d(490) values showed reliable estimates in case of both methods. The results indicate that for band ratio algorithms, the root mean square error (RMSE) decreases and the coefficient of determination (R-2) increases when using longer wavelengths in the visible spectrum as a reference band. It was found that the best estimates were retrieved from MERIS data when using the ratio of R-rs(490)/R-rs(709) for coastal waters (K-d(490) < 2.5 m(-1)) and the ratio R-rs(560)/R-rs(709) for more turbid inland waters (Kd(490) > 2.5 m(-1)). As a result, a combined band ratio algorithm was developed, which provides a promising approach R-2 = 0.98, RMSE= 17%, N = 34, p < 0.05) for estimating K-d(490) over a wide range of values (0.3-6.1 m(-1)).

Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetrask in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Tornetrask. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.

Seagrass beds are highly productive coastal ecosystems that sustain a rich and diverse associated fauna and flora. Increasing anthropogenic pressures threaten seagrass ecosystems and have already led to major seagrass losses across the world. Marine Protected Areas (MPAs) have become one of the key strategies to manage coastal ecosystems and associated resources worldwide and have been often shown to successfully protect marine ecosystems. However, relatively few studies have assessed the effects of MPAs on seagrass ecosystems, and there are indications that MPAs may not be able to fully protect seagrasses, especially from disturbances originating outside their boundaries. Within this context, this thesis aimed to investigate the direct and indirect effects (those mediated by biotic interactions) of MPAs on tropical seagrasses, associated fish communities, and ecosystem processes.

The thesis consists of three parts. First, we used 10-years of seagrass monitoring data within a MPA to evaluate the temporal variability in seagrass cover and species composition in relation to changes in environmental conditions (Paper I). Second, we investigated the potential of MPAs to enhance the temporal stability of seagrass ecosystems using a 10-month field study. We surveyed seagrass-associated fish communities (Paper II) and estimated seagrass growth and herbivory rates (Paper III) during three different seasons within MPAs and unprotected sites. Finally, to evaluate the effects of MPAs and land-use on seagrass ecosystems we surveyed seagrass species and trait composition within government-managed MPAs, community-managed MPAs, and unprotected sites (Paper IV).

The seagrass bed monitored in Paper I showed a high temporal and spatial variability, with a temporal decline in cover and change in species composition, followed by a period of recovery. This pattern could not be associated with any of the climate and tidal variables considered, suggesting that potential drivers of decline may have originated outside MPA boundaries. The results from the seasonal field study showed that MPAs increased the temporal stability of seagrass-associated fish communities, particularly juvenile fish (Paper II), and strengthened a positive link between herbivorous fish, herbivory rates, and seagrass growth (Paper III), suggesting the presence of a positive feedback that promotes stability. Finally, MPAs affected seagrass species and trait composition (by selecting for more stress-sensitive species) but did not seem to be able to protect seagrasses from land-use effects, with seagrasses showing similar changes in species and trait composition within and outside MPAs (Paper IV). Considering these results, this thesis builds to a body of literature indicating that MPAs alone may not be sufficient to protect seagrass ecosystems and that improved management strategies may be necessary to preserve these important coastal habitats.

In a changing environment, there is an increasing interest to monitor ecosystems to understand their responses to environmental change. Seagrass meadows are highly important ecosystems, but at the same time they are under a constant threat from human activities, as well as climate impacts, and marked declines have been observed worldwide. Despite increasing efforts, monitoring of multi-specific tropical seagrass meadows is scarce, particularly in developing regions. Here we analysed data from the first 10 years of a monitoring programme in a marine protected area in Zanzibar (Tanzania) to assess temporal changes in seagrass cover and species composition and to detect potential drivers of change. The seagrass meadow experienced a strong gradual decline in seagrass cover and changes in species composition, followed by a period of recovery. However, the timing and length of these temporal patterns varied in space (between transects). Of the climate variables considered, cloud cover, temperature, storm occurrence, sunspot activity and the height of the diurnal low tide seemed to influence seagrass cover, although only to a small extent, suggesting that the monitored seagrass meadow may be influenced by other unmeasured factors. Considering our results, seagrass meadows seem to be highly dynamic at small spatial scales even in the absence of major local anthropogenic impacts. Further monitoring programmes should be developed in the region to gain a better understanding of seagrass temporal variability and causes of change.

Seagrass beds are highly important for tropical ecosystems by supporting abundant and diverse fish assemblages that form the basis for artisanal fisheries. Although a number of local- and regional-scale variables are known to influence the abundance, diversity and assemblage structure of seagrass-associated fish assemblages, few studies have evaluated the relative and joint (interacting) influences of variables, especially those acting at different scales. Here, we examined the relative importance of local- and regional-scale factors structuring seagrass-associated fish assemblages, using a field survey in six seagrass (Thalassodendron ciliatum) areas around Unguja Island (Zanzibar, Tanzania). Fish density and assemblage structure were mostly affected by two regional-scale variables; distance to coral reefs, which positively affected fish density, and level of human development, which negatively affected fish density. On the local scale, seagrass biomass had a positive (but weaker) influence on fish density. However, the positive effect of seagrass biomass decreased with increasing level of human development. In summary, our results highlight the importance of assessing how multiple local and regional variables, alone and together, influence fish communities, in order to improve management of seagrass ecosystems and their services.

Herbivory is a key process influencing the structure and function of both terrestrial and aquatic systems. In seagrass ecosystems, moderate levels of herbivory may stimulate plant growth, compensating for the loss of eaten tissue. However, the relationship between herbivory and seagrass growth can be influenced by an array of factors, such as seasonality, herbivore abundance, and presence of epiphytes, many of which can be directly or indirectly affected by human activities like fishing. Here, we used data from a multi-season field survey in fished and protected seagrass beds to assess how fishing and seasonality affect the link between herbivores, herbivory, and plant growth in seagrasses. Path analyses revealed an interactive effect of seasonality and protection. In protected seagrass beds, seasonally high herbivore abundance positively affected herbivory rates, which in turn enhanced seagrass growth. This link was however not apparent in seagrass beds subjected to fishing activities. At the same time, seasonality effects seemed stronger in fished areas, suggesting that in addition to weakening a positive herbivory-plant growth interaction, fishing increases temporal instability of ecosystems. Our results highlight the need for evaluating not only the direct effects of fisheries exploitation on fish populations, but also the potential indirect effects on ecosystems, to improve fisheries management.

Marine protected areas (MPAs) have been shown to increase long-term temporal stability of fish communities and enhance ecosystem resilience to anthropogenic disturbance. Yet, the potential ability of MPAs to buffer effects of environmental variability at shorter time scales remains widely unknown. In the tropics, the yearly monsoon cycle is a major natural force affecting marine organisms in tropical regions, and its timing and severity are predicted to change over the coming century, with potentially severe effects on marine organisms, ecosystems and ecosystem services. Here, we assessed the ability of MPAs to buffer effects of monsoon seasonality on seagrass-associated fish communities, using a field survey in two MPAs (no-take zones) and two unprotected (open-access) sites around Zanzibar (Tanzania). We assessed the temporal stability of fish density and community structure within and outside MPAs during three monsoon seasons in 2014-2015, and investigated several possible mechanisms that could regulate temporal stability. Our results show that MPAs did not affect fish density and diversity, but that juvenile fish densities were temporally more stable within MPAs. Second, fish community structure was more stable within MPAs for juvenile and adult fish, but not for subadult fish or the total fish community. Third, the observed effects may be due to a combination of direct and indirect (seagrass-mediated) effects of seasonality and, potentially, fluctuating fishing pressure outside MPAs. In summary, these MPAs may not have the ability to enhance fish density and diversity and to buffer effects of monsoon seasonality on the whole fish community. However, they may increase the temporal stability of certain groups, such as juvenile fish. Consequently, our results question whether MPAs play a general role in the maintenance of biodiversity and ecosystem functioning under changing environmental conditions in tropical seagrass fish communities.

In this study, we modelled population responses to chronic external gamma radiation in 12 laboratory species (including aquatic and soil invertebrates, fish and terrestrial mammals). Our aim was to compare radiosensitivity between individual and population endpoints and to examine how internationally proposed benchmarks for environmental radioprotection protected species against various risks at the population level. To do so, we used population matrix models, combining life history and chronic radiotoxicity data (derived from laboratory experiments and described in the literature and the FRED ERICA database) to simulate changes in population endpoints (net reproductive rate R-0, asymptotic population growth rate lambda, equilibrium population size N-eq) for a range of dose rates. Elasticity analyses of models showed that population responses differed depending on the affected individual endpoint (juvenile or adult survival, delay in maturity or reduction in fecundity), the considered population endpoint (R-0, lambda or N-eq) and the life history of the studied species. Among population endpoints, net reproductive rate R-0 showed the lowest EDR10 (effective dose rate inducing 10% effect) in all species, with values ranging from 26 mu Gy h(-1) in the mouse Mus musculus to 38,000 mu Gy h(-1) in the fish Oryzias latipes. For several species, EDR10 for population endpoints were lower than the lowest EDR10 for individual endpoints. Various population level risks, differing in severity for the population, were investigated. Population extinction (predicted when radiation effects caused population growth rate lambda to decrease below 1, indicating that no population growth in the long term) was predicted for dose rates ranging from 2700 mu Gy h(-1) in fish to 12,000 mu Gy h(-1) in soil invertebrates. A milder risk, that population growth rate lambda will be reduced by 10% of the reduction causing extinction, was predicted for dose rates ranging from 24 mu Gy h(-1) in mammals to 1800 mu Gy h(-1) in soil invertebrates. These predictions suggested that proposed reference benchmarks from the literature for different taxonomic groups protected all simulated species against population extinction. A generic reference benchmark of 10 mu Gy h(-1) protected all simulated species against 10% of the effect causing population extinction. Finally, a risk of pseudo-extinction was predicted from 2.0 mu Gy h(-1) in mammals to 970 mu Gy h(-1) in soil invertebrates, representing a slight but statistically significant population decline, the importance of which remains to be evaluated in natural settings.

The combined effects of the herbicide glyphosate and elevated temperature were studied on the tropical staghorn coral Acropora formosa, in Nha Trang bay, Vietnam. The corals were collected from two different reefs, one close to a polluted fish farm and one in a marine-protected area (MPA). In the laboratory, branches of the corals were exposed to the herbicide glyphosate at ambient (28 degrees C) and at 3 degrees C elevated water temperatures (31 degrees C). Effects of herbicide and elevated temperature were studied on coral bleaching using photography and digital image analysis (new colorimetric method developed here based on grayscale), chlorophyll a analysis, and symbiotic dinoflagellate (Symbiodinium, referred to as zooxanthellae) counts. All corals from the MPA started to bleach in the laboratory before they were exposed to the treatments, indicating that they were very sensitive, as opposed to the corals collected from the more polluted site, which were more tolerant and showed no bleaching response to temperature increase or herbicide alone. However, the combined exposure to the stressors resulted in significant loss of color, proportional to loss in chlorophyll a and zooxanthellae. The difference in sensitivity of the corals collected from the polluted site versus the MPA site could be explained by different symbiont types: the resilient type C3u and the stress-sensitive types C21 and C23, respectively. The additive effect of elevated temperatures and herbicides adds further weight to the notion that the bleaching of coral reefs is accelerated in the presence of multiple stressors. These results suggest that the corals in Nha Trang bay have adapted to the ongoing pollution to become more tolerant to anthropogenic stressors, and that multiple stressors hamper this resilience. The loss of color and decrease of chlorophyll a suggest that bleaching is related to concentration of chloro-pigments. The colorimetric method could be further fine-tuned and used as a precise, non-intrusive tool for monitoring coral bleaching in situ.

Germ layer formation and axial patterning are biological processes that are tightly linked during embryonic development of most metazoans. In addition to canonical WNT, it has been proposed that ERK-MAPK signaling is involved in specifying oral as well as aboral territories in cnidarians. However, the effector and the molecular mechanism underlying latter phenomenon is unknown. By screening for potential effectors of ERK-MAPK signaling in both domains, we identified a member of the ETS family of transcription factors, Nverg that is bipolarily expressed prior to gastrulation. We further describe the crucial role of NvERG for gastrulation, endomesoderm as well as apical domain formation. The molecular characterization of the obtained NvERG knock-down phenotype using previously described as well as novel potential downstream targets, provides evidence that a single transcription factor, NvERG, simultaneously controls expression of two different sets of downstream targets, leading to two different embryonic gene regulatory networks (GRNs) in opposite poles of the developing embryo. We also highlight the molecular interaction of cWNT and MEK/ERK/ERG signaling that provides novel insight into the embryonic axial organization of Nematostella, and show a cWNT repressive role of MEK/ERK/ERG signaling in segregating the endomesoderm in two sub-domains, while a common input of both pathways is required for proper apical domain formation. Taking together, we build the first blueprint for a global cnidarian embryonic GRN that is the foundation for additional gene specific studies addressing the evolution of embryonic and larval development.

Phytoplankton and heterotrophic bacteria are key groups at the base of aquatic food webs. In estuaries receiving riverine water with a high content of coloured allochthonous dissolved organic matter (ADOM), phytoplankton primary production may be reduced, while bacterial production is favoured. We tested this hypothesis by performing a field study in a northerly estuary receiving nutrient-poor, ADOM-rich riverine water, and analyzing results using multivariate statistics. Throughout the productive season, and especially during the spring river flush, the production and growth rate of heterotrophic bacteria were stimulated by the riverine inflow of dissolved organic carbon (DOC). In contrast, primary production and photosynthetic efficiency (i.e. phytoplankton growth rate) were negatively affected by DOC. Primary production related positively to phosphorus, which is the limiting nutrient in the area. In the upper estuary where DOC concentrations were the highest, the heterotrophic bacterial production constituted almost 100% of the basal production (sum of primary and bacterial production) during spring, while during summer the primary and bacterial production were approximately equal. Our study shows that riverine DOC had a strong negative influence on coastal phytoplankton production, likely due to light attenuation. On the other hand DOC showed a positive influence on bacterial production since it represents a supplementary food source. Thus, in boreal regions where climate change will cause increased river inflow to coastal waters, the balance between phytoplankton and bacterial production is likely to be changed, favouring bacteria. The pelagic food web structure and overall productivity will in turn be altered.

Despite cyanobacteria being a key phytoplankton group in the Baltic Sea, the factors governing their community structure are still poorly understood. Here, we studied the occurrence of the orders Chroococcales, Oscillatoriales and Nostocales, and potentially explanatory variables at five locations in the northern Baltic Sea from June September, 1998-2012. Cyanobacteria constituted 1-36% of the total phytoplankton biomass along the north south gradient. In the Bothnian Bay, Chroococcales and Oscillatoriales dominated the cyanobacterial community, whereas in the Bothnian Sea and northern Baltic Proper, Nostocales was the dominant group. The dominance of Chroococcales was coupled to low salinity and low total phosphorus, whereas Oscillatoriales correlated with high total nitrogen and low salinity. Nostocales correlated to high total phosphorus, inorganic phosphorus and salinity. Chroococcales showed an increase over time in the offshore Bothnian Bay, whereas Nostocales increased in the coastal Bothnian Sea and coastal Baltic Proper. The increase of Nostocales in the coastal Bothnian Sea was explained by a rise in total phosphorus and decrease in dissolved inorganic nitrogen compared to an increase of total nitrogen and phosphorus in the coastal Baltic Proper. No significant trends were observed in the cyanobacterial community in the offshore Bothnian Sea and the offshore northern Baltic Proper. We concluded that Chroococcales may be a useful indicator for increased phosphorus levels in waters with low phosphorus concentrations, whereas Nostocales could be used as a quality indicator for increasing phosphorus concentrations in waters with low inorganic N/P ratios (< 20), such as in the coastal Bothnian Sea and Baltic Proper.

Climate change is likely to have large effects on the Baltic Sea ecosystem. Simulations indicate 2-4 degrees C warming and 50-80 % decrease in ice cover by 2100. Precipitation may increase similar to 30 % in the north, causing increased land runoff of allochthonous organic matter (AOM) and organic pollutants and decreased salinity. Coupled physical-biogeochemical models indicate that, in the south, bottom-water anoxia may spread, reducing cod recruitment and increasing sediment phosphorus release, thus promoting cyanobacterial blooms. In the north, heterotrophic bacteria will be favored by AOM, while phytoplankton production may be reduced. Extra trophic levels in the food web may increase energy losses and consequently reduce fish production. Future management of the Baltic Sea must consider the effects of climate change on the ecosystem dynamics and functions, as well as the effects of anthropogenic nutrient and pollutant load. Monitoring should have a holistic approach, encompassing both autotrophic (phytoplankton) and heterotrophic (e.g., bacterial) processes.

Plant patch structure and environmental context can influence the outcome of antagonistic and mutualistic plant-insect interactions, leading to spatially variable fitness effects for plants. We investigated the effects of herbivory and pollen limitation on plant reproductive performance in 28 patches of the self-compatible perennial herb Scrophularia nodosa and assessed how such effects varied with plant patch size, plant density and tree cover. Both antagonistic and mutualistic interactions had strong effects on plant reproductive performance. Leaf feeding from herbivores reduced both fruit production and seed germination, and leaf herbivory increased with plant patch size. Experimentally hand-pollinated flowers produced more seeds than open-pollinated flowers, and pollen limitation was more severe in patches with fewer plants. Our study on S. nodosa is one of few which documents that plant patch structure influences the outcome of both antagonistic and mutualistic plant-insect interactions. The results thus provide an example of how variation in plant patch structure and environmental factors can lead to spatially variable fitness effects from mutualistic and antagonistic interactions.

Habitat area is an important predictor of spatial variation in animal densities. However, the area often correlates with the quantity of resources within habitats, complicating our understanding of the factors shaping animal distributions. We addressed this problem by investigating densities of insect herbivores in habitat patches with a constant area but varying numbers of plants. Using a mathematical model, predictions of scale-dependent immigration and emigration rates for insects into patches with different densities of host plants were derived. Moreover, a field experiment was conducted where the scaling properties of odour-mediated attraction in relation to the number of odour sources were estimated, in order to derive a prediction of immigration rates of olfactory searchers. The theoretical model predicted that we should expect immigration rates of contact and visual searchers to be determined by patch area, with a steep scaling coefficient, mu = -1. The field experiment suggested that olfactory searchers should show a less steep scaling coefficient, with mu a parts per thousand -0.5. A parameter estimation and analysis of published data revealed a correspondence between observations and predictions, and density-variation among groups could largely be explained by search behaviour. Aphids showed scaling coefficients corresponding to the prediction for contact/visual searchers, whereas moths, flies and beetles corresponded to the prediction for olfactory searchers. As density responses varied considerably among groups, and variation could be explained by a certain trait, we conclude that a general theory of insect responses to habitat heterogeneity should be based on shared traits, rather than a general prediction for all species.

When searching for resources in heterogeneous environments, animals must rely on their abilities to detect the resources via their sensory systems. However, variation in the strength of the sensory cue may be mediated by the physical size of the resource patch. Patch detection of insects are often predicted by the scaling of sensory cues to patch size, where visual cues has been proposed to scale proportional to the diameter of the patch. The scaling properties of olfactory cues are, however, virtually unknown. Here, we investigated scaling rules for olfactory information in a gradient of numbers of odour sources, relevant to odour-mediated attraction under field conditions. We recorded moth antennal responses to sex pheromones downwind from pheromone patches and estimated the slope in the scaling relationship between the effective length of the odour plumes and the number of odour sources. These measurements showed that the effective plume length increased proportional to the square root of the number of odour sources. The scaling relationship, as estimated in the field experiment, was then evaluated against field data of the slope in the relationship between trap catch and release rate of chemical attractants for a wide range of insects. This meta-analysis revealed an average slope largely consistent with the estimated scaling relationship between the effective plume length and the number of odour sources. This study is the first to estimate the scaling properties of olfactory cues empirically and has implications for understanding and predicting the spatial distributions of insects searching by means of olfactory cues in heterogeneous environments.

The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994-2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems.

Farmers' practices in the management of agricultural landscapes influence biodiversity with implications for livelihoods, ecosystem service provision, and biodiversity conservation. In this study, we examined how smallholding farmers in an agriculture-forest mosaic landscape in southwestern Ethiopia manage trees and forests with regard to a few selected ecosystem services and disservices that they highlighted as beneficial or problematic. Qualitative and quantitative data were collected from six villages, located both near and far from forest, using participatory field mapping and semistructured interviews, tree species inventory, focus group discussions, and observation. The study showed that farmers' management practices, i.e., the planting of trees on field boundaries amid their removal from inside arable fields, preservation of trees in semimanaged forest coffee, maintenance of patches of shade coffee fields in the agricultural landscape, and establishment of woodlots with exotic trees result in a restructuring of the forest-agriculture mosaic. In addition, the strategies farmers employed to mitigate crop damage by wild mammals such as baboons and bush pigs, e. g., migration and allocation of migrants on lands along forests, have contributed to a reduction in forest and tree cover in the agricultural landscape. Because farmers' management practices were overall geared toward mitigating the negative impact of disservices and to augment positive services, we conclude that it is important to operationalize ecosystem processes as both services and disservices in studies related to agricultural landscapes.

In dioecious species with both sexual and asexual reproduction, the spatial distribution of individual clones affects the potential for sexual reproduction and local adaptation. The seaweed Fucus radicans, endemic to the Baltic Sea, has separate sexes, but new attached thalli may also form asexually. We mapped the spatial distribution of clones (multilocus genotypes, MLGs) over macrogeographic (>500km) and microgeographic (<100m) scales in the Baltic Sea to assess the relationship between clonal spatial structure, sexual recruitment, and the potential for natural selection. Sexual recruitment was predominant in some areas, while in others asexual recruitment dominated. Where clones of both sexes were locally intermingled, sexual recruitment was nevertheless low. In some highly clonal populations, the sex ratio was strongly skewed due to dominance of one or a few clones of the same sex. The two largest clones (one female and one male) were distributed over 100-550km of coast and accompanied by small and local MLGs formed by somatic mutations and differing by 1-2 mutations from the large clones. Rare sexual events, occasional long-distance migration, and somatic mutations contribute new genotypic variation potentially available to natural selection. However, dominance of a few very large (and presumably old) clones over extensive spatial and temporal scales suggested that either these have superior traits or natural selection has only been marginally involved in the structuring of genotypes.

Closely related taxa provide significant case studies for understanding evolution of new species but may simultaneously challenge species identification and definition. In the Baltic Sea, two dominant and perennial brown algae share a very recent ancestry. Fucus vesiculosus invaded this recently formed postglacial sea 8000 years ago and shortly thereafter Fucus radicans diverged from this lineage as an endemic species. In the Baltic Sea both species reproduce sexually but also recruit fully fertile new individuals by asexual fragmentation. Earlier studies have shown local differences in morphology and genetics between the two taxa in the northern and western Bothnian Sea, and around the island of Saaremaa in Estonia, but geographic patterns seemin conflict with a single origin of F. radicans. To investigate the relationship between northern and Estonian distributions, we analysed the genetic variation using 9 microsatellite loci in populations from eastern Bothnian Sea, Archipelago Sea and the Gulf of Finland. These populations are located in between earlier studied populations. However, instead of bridging the disparate genetic gap between N-W Bothnian Sea and Estonia, as expected from a simple isolation-by-distance model, the new populations substantially increased overall genetic diversity and showed to be strongly divergent from the two earlier analysed regions, showing signs of additional distinct populations. Contrasting earlier findings of increased asexual recruitment in low salinity in the Bothnian Sea, we found high levels of sexual reproduction in some of the Gulf of Finland populations that inhabit extremely low salinity. The new data generated in this study supports the earlier conclusion of two reproductively isolated but very closely related species. However, the new results also add considerable genetic and morphological complexity within species. This makes species separation at geographic scales more demanding and suggests a need for more comprehensive approaches to further disentangle the intriguing relationship and history of the Baltic Sea fucoids.

Costa Rica is a tropical country with one of the highest biodiversity on Earth. It also has an intensive agriculture, and pesticide runoff from banana and pineapple plantations may cause a high toxicity risk to non-target species in rivers downstream the plantations. We performed a first tier risk assessment of the maximum measured concentrations of 32 pesticides detected over 4 years in the River Madre de Dios (RMD) and its coastal lagoon on the Caribbean coast of Costa Rica. Species sensitivity distributions (SSDs) were plotted in order to derive HC5 values for each pesticide, i.e., hazard concentrations for 5 % of the species, often used as environmental criteria values in other countries. We also carried out toxicity tests for selected pesticides with native Costa Rican species in order to calculate risk coefficients according to national guidelines in Costa Rica. The concentrations of herbicides diuron and ametryn and insecticides carbofuran, diazinon, and ethoprophos exceeded either the HC5 value or the lower limit of its 90 % confidence interval suggesting toxic risks above accepted levels. Risk coefficients of diuron and carbofuran derived using local guidelines indicate toxicity risks as well. The assessed fungicides did not present acute toxic risks according to our analysis. Overall, these results show a possible toxicity of detected pesticides to aquatic organisms and provide a comparison of Costa Rican national guidelines with more refined methods for risk assessment based on SSDs. Further higher tier risk assessments of pesticides in this watershed are also necessary in order to consider pesticide water concentrations over time, toxicity from pesticide mixtures, and eventual effects on ecosystem functions.

Understanding and disentangling different processes underlying the assembly and diversity of communities remains a key challenge in ecology. Species can assemble into communities either randomly or due to deterministic processes. Deterministic assembly leads to species being more similar (underdispersed) or more different (overdispersed) in certain traits than would be expected by chance. However, the relative importance of those processes is not well understood for many organisms, including terrestrial invertebrates. Based on knowledge of a broad range of species traits, we tested for the presence of trait underdispersion (indicating dispersal or environmental filtering) and trait overdispersion (indicating niche partitioning) and their relative importance in explaining land snail community composition on lake islands. The analysis of community assembly was performed using a functional diversity index (Rao's quadratic entropy) in combination with a null model approach. Regression analysis with the effect sizes of the assembly tests and environmental variables gave information on the strength of under- and overdispersion along environmental gradients. Additionally, we examined the link between community weighted mean trait values and environmental variables using a CWM-RDA. We found both trait underdispersion and trait overdispersion, but underdispersion (eight traits) was more frequently detected than overdispersion (two traits). Underdispersion was related to four environmental variables (tree cover, habitat diversity, productivity of ground vegetation, and location on an esker ridge). Our results show clear evidence for underdispersion in traits driven by environmental filtering, but no clear evidence for dispersal filtering. We did not find evidence for overdispersion of traits due to diet or body size, but overdispersion in shell shape may indicate niche differentiation between snail species driven by small-scale habitat heterogeneity. The use of species traits enabled us to identify key traits involved in snail community assembly and to detect the simultaneous occurrence of trait underdispersion and overdispersion.

Variation in food stoichiometry affects individual performance and population dynamics, but it is also likely that species with different life histories should differ in their sensitivity to food stoichiometry. To address this question, we investigated the ability of the three nettle-feeding butterflies (Aglais urticae, Polygonia c-album, and Aglais io) to respond adaptively to induced variation in plant stoichiometry in terms of larval performance. We hypothesized that variation in larval performance between plant fertilization treatments should be functionally linked to species differences in host plant specificity. We found species-specific differences in larval performance between plant fertilization treatments that could not be explained by nutrient limitation. We showed a clear evidence of a positive correlation between food stoichiometry and development time to pupal stage and pupal mass in Aglais urticae. The other two species showed a more complex response. Our results partly supported our prediction that host plant specificity affects larval sensitivity to food stoichiometry. However, we suggest that most of the differences observed may instead be explained by differences in voltinism (number of generations per year). We believe that the potential of some species to respond adaptively to variation in plant nutrient content needs further attention in the face of increased eutrophication due to nutrient leakage from human activities.

Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7x10(-5). A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach.

Species are normally considered to be the fundamental unit for understanding the evolution of biodiversity. Yet, in a survey of botanists in 1940, twice as many felt that plant genera were more natural units than plant species. Revisiting the survey, we found more people now regarded species as a more evolutionarily real unit, but a sizeable number still felt that genera were more evolutionarily real than species. Definitions of evolutionarily real' split into those based on shared evolutionary history and those based on shared evolutionary fate via ongoing evolutionary processes. We discuss recent work testing for shared evolutionary fate at the species and higher levels and present preliminary evidence for evolutionarily significant higher taxa in plants.

Casuarina glauca is an actinorhizal tree which establishes root-nodule symbiosis with N-2-fixing Frankia bacteria. This plant is commonly found in saline zones and is widely used to remediate marginal soils and prevent desertification. The nature of its ability to survive in extreme environments and the extent of Frankia contribution to stress tolerance remain unknown. Thus, we evaluated the ability of C. glauca to cope with salt stress and the influence of the symbiosis on this trait. To this end, we analysed the impact of salt on plant growth, mineral contents, water relations, photosynthetic-related parameters and nonstructural sugars in nodulated vs. non-nodulated plants. Although the effects on photosynthesis and stomatal conductance started to become measurable in the presence of 200 mM NaCl, photochemical (e.g., photosynthetic electron flow) and biochemical (e.g., activity of photosynthetic enzymes) parameters were only strongly impaired when NaCl levels reached 600 mM. These results indicate the maintenance of high tissue hydration under salt stress, probably associated with enhanced osmotic potential. Furthermore, the maintenance of photosynthetic assimilation potential (A(max)), together with the increase in the quantum yield of down-regulated energy dissipation of PSII (Y-NPQ), suggested a down-regulation of photosynthesis instead of photo-damaging effects. A comparison of the impact of increasing NaCl levels on the activities of photosynthetic (RubisCO and ribulose-5 phosphate kinase) and respiratory (pyruvate kinase and NADH-dependent malate dehydrogenase) enzymes vs. photosynthetic electron flow and fluorescence parameters, revealed that biochemical impairments are more limiting than photochemical damage. Altogether, these results indicate that, under controlled conditions, C glauca tolerates high NaCl levels and that this capacity is linked to photosynthetic adjustments.

In natural waters, dissolved oxyanions often dominate over the particle-bound element fraction. Still, the scavenging of oxyanions by suspended particles might contribute significantly to their dynamic cycling and distribution. To investigate how oxyanions are affected by manganese (Mn) redox cycling, detailed depth profiles across the pelagic redox zone at the Landsort Deep, Baltic Sea, were collected for molybdenum (Mo), vanadium (V), and tungsten (W), for both dissolved (< 0.22 mu m) and suspended particulate (> 0.22 mu m) fractions. All three oxyanions show a non-conservative behavior in the stratified Landsort Deep. Strong linear correlations with Mn in the particulate fraction in the redox zone of the Landsort Deep suggest that Mn redox cycling influences their distribution. In the dissolved fraction, Mo, V, and W exhibited rather different behavior. Molybdenum was depleted below the redox zone, while V was depleted only within the redox zone. Tungsten concentrations increased within the redox zone, being three times higher in the sulfidic zone than in the surface water. Unlike Mo, W shows no tendency for adsorption or co-precipitation under the prevailing weak sulfidic conditions in the deep water of the Landsort Deep and is, therefore, not exported to the underlying sediment. The Landsort Deep data were compared with data from the northern Baltic Sea (Bothnian Bay, Kalix River and Rane River estuaries), where particulate iron (Fe) occurs in high abundance. The particulate fractions of Mo, V, and W decreased during mixing in these estuaries. Vanadium showed the most drastic reduction, with a decrease in dissolved and particulate fractions, indicating that different processes influence the distribution of these oxyanions.

The mechanistic basis of feather moss-cyanobacteria associations, a main driver of nitrogen (N) input into boreal forests, remains unknown. Here, we studied colonization by Nostoc sp. on two feather mosses that form these associations (Pleurozium schreberi and Hylocomium splendens) and two acrocarpous mosses that do not (Dicranum polysetum and Polytrichum commune). We also determined how N availability and moss reproductive stage affects colonization, and measured N transfer from cyanobacteria to mosses. The ability of mosses to induce differentiation of cyanobacterial hormogonia, and of hormogonia to then colonize mosses and re-establish a functional symbiosis was determined through microcosm experiments, microscopy and acetylene reduction assays. Nitrogen transfer between cyanobacteria and Pleurozium schreberi was monitored by secondary ion mass spectrometry (SIMS). All mosses induced hormogonia differentiation but only feather mosses were subsequently colonized. Colonization on Pleurozium schreberi was enhanced during the moss reproductive phase but impaired by elevated N. Transfer of N from cyanobacteria to their host moss was observed. Our results reveal that feather mosses likely secrete species-specific chemo-attractants when N-limited, which guide cyanobacteria towards them and from which they gain N. We conclude that this signalling is regulated by N demands of mosses, and serves as a control of N input into boreal forests.

Stable isotope analysis (SIA) has emerged as an important tool for understanding consumer diets and diet shifts. However, although the general idea behind SIA is clear, the interpretation of data is often fraught with problems because tissue turnover and fractionations are not known. We investigated shifts in stable isotope composition of spiders following a diet shift, using mealworms fed either maize (C4) or wheat (C3) flour. Mealworms had different carbon isotope composition depending on their diet and this difference was reflected in spider body parts. In the experiment, we first fed the spiders on a diet of either maize-fed or wheat-fed mealworms and then switched diet at the time of the second molt. Spiders were then sampled repeatedly until the next molt. We sampled both legs and abdomens, as these are presumed to have different turnover of tissue, and also molt remains were sampled when this was relevant. The data indicated that the spider legs had a turnover of about 20days, whereas the spider abdomens had a turnover of about 8days. Molt remains had the slowest turnover and reflected the diet at the previous molt, when the exoskeleton was formed. Both these observations indicate that SIA may be successfully used for elucidating diet shifts. More problematic was the fact that fractionation of carbon isotope ratios varied with body parts and diets. When spiders were fed maize-mealworms then the fractionation was larger for abdomens, but when the spiders were fed wheat-mealworms then the fractionation was larger for legs. The mechanisms underlying this pattern are unclear and deserve further attention.

This PhD study focusses on the use of MEdium Resolution Imaging Spectrometer (MERIS) data for reliable and quantitative water-quality assessment of optically-complex waters (lake, brackish and coastal waters). The thesis is divided into two parts: A. intercalibration of reflectance measurements in different optically-complex water bodies (Paper I), and validation of various satellite processing algorithms for the coastal zone (Paper II). B. Applications: the use of MERIS data in integrated coastal zone management mostly using Himmerfjärden bay as an example.

Himmerfjärden bay is one of the most frequently monitored coastal areas in the world and it is also the recipient of a large urban sewage treatment plant, where a number of full-scale nutrient management experiments have been conducted to evaluate the ecological changes due to changes in nutrient schemes in the sewage plant.

Paper I describes the development and assessment of a new hyperspectral handheld radiometer for in situ sampling and validation of remote sensing reflectance. The instrument is assessed in comparison with readily available radiometers that are commonly used in validation.

Paper II has a focus on the validation of level 2 reflectance and water products derived from MERIS data. It highlights the importance of calibration and validation activities, and the current accuracy and limitations of satellite products in the coastal zone. Bio-optical in situ data is highlighted as one of the key components for assessing the reliability of current and future satellite missions. Besides suspended particulate matter (SPM), the standard MERIS products have shown to be insufficient to assure data quality retrieval for Baltic Sea waters. Alternative processors and methods such as those assessed and developed in this thesis therefore will have to be put in place in order to secure the success of future operational missions, such as Sentinel-3.

The two presented manuscripts in the applied part B of the thesis (paper III and IV), showed examples on the combined use of in situ measurements with optical remote sensing to support water quality monitoring programs by using turbidity and suspended particulate matter as coastal indicators (manuscript III). The article also provides a new turbidity algorithm for the Baltic Sea and a robust and cost-efficient method for research and management. A novel approach to improve the quality of the satellite-derived products in the coastal zone was demonstrated in manuscript IV. The analysis included, the correction for adjacency effects from land and an improved pixel quality screening. The thesis provides the first detailed spatio-temporal description of the evolution of phytoplankton blooms in Himmerfjärden bay using quality-assured MERIS data, thus forwarding our understanding of ecological processes in in Swedish coastal waters.

It must be noted that monitoring from space is not a trivial matter in these optically-complex waters dominated by the absorption of coloured dissolved organic matter (CDOM). These types of coastal waters are especially challenging for quantitative assessment from space due to their low reflectance. Papers III and IV thus also provide tools for a more versatile use in other coastal waters that are not as optically-complex as the highly absorbing Baltic Sea waters. The benefits of the increased spatial-temporal data coverage by optical remote sensing were presented, and also compared to in situ sampling methods (using chlorophyll-a as indicator).

The thesis addresses validation activities associated with the use of in situ and satellite-based radiometers to assess water quality parameters, such as chlorophyll-a (Chl-a), total suspended matter (TSM) and coloured dissolved organic matter (CDOM- also known as yellow substances, YEL) in CDOM-dominated waters. In paper I, an inter-comparison of in situ radiometers is presented. Here, a new hand-held radiometer, the Water Insight Spectrometer (WISP-3) was tested and evaluated for routine water monitoring against other common radiometers used for validation. The WISP-3 measures the reflectance at the surface, and thus also works in shallow depths. The WISP-3 is designed for validation in places where other radiometers are difficult to deploy. As it is hyperspectral it can be used to develop in-water algorithms for the retrieval of water-quality information. In paper II, satellite data from the 3rd reprocessing archives of the MEdium Resolution Imaging Spectrometer (MERIS) sensor on board of ENVISAT is evaluated. MERIS level 2 reflectance and water products are assessed against in situ data. This assessment is required in order to ensure the reliability of monitoring systems based on MERIS data such as the Swedish coastal and lake monitoring system www.vattenkvalitet.se. The evaluation of reflectance data is based on a pair-wise comparison of the standard MEGS processor and three coastal processors that are provided as source free plug-ins for the VISAT BEAM software; all pairs are compared to data measured in situ. The derived water products are evaluated both on a pair-wise comparison of processors as well as on an individual comparison of some processors to sea-truthing data. The studied processors improved the retrievals of MERIS reflectance when used the latest MERIS FR 3rd reprocessing, equalized and “smile” corrected and a land adjacency effects were corrected using the improved contrast between ocean and land (ICOL). The blue spectral bands remain problematic for all processors. Chlorophyll was retrieved best using FUB with an overestimation between 18% - 26.5% (MNB) dependent on the compared pairs. At low chlorophyll < 2.5 mg m-3, random errors dominates the retrievals of MEGS. MEGS showed lower bias and random errors when deriving suspended particulate matter (SPM) with an overestimation in the range 8-16% (MNB). All processors failed to retrieve CDOM correctly, but FUB could at least resolve variations in CDOM, however with a systematic underestimation that may be corrected for by using a local correction factor . MEGS has shown already potential to be used as operational processor in the Himmerfjärden bay and adjacent areas, but it requires further improvement of the atmospheric correction for the blue bands and better definition at relatively low chlorophyll concentrations in presence of CDOM.

In this study, retrievals of the medium resolution imaging spectrometer (MERIS) reflectances and water quality products using four different coastal processing algorithms freely available are assessed by comparison against sea-truthing data. The study is based on a pair-wise comparison using processor-dependent quality flags for the retrieval of valid common macro-pixels. This assessment is required in order to ensure the reliability of monitoring systems based on MERIS data, such as the Swedish coastal and lake monitoring system (http://vattenkvalitet.se). The results show that the pre-processing with the Improved Contrast between Ocean and Land (ICOL) processor, correcting for adjacency effects, improves the retrieval of spectral reflectance for all processors. Therefore, it is recommended that the ICOL processor should be applied when Baltic coastal waters are investigated. Chlorophyll was retrieved best using the FUB (Free University of Berlin) processing algorithm, although overestimations in the range 18-26.5 %, dependent on the compared pairs, were obtained. At low chlorophyll concentrations (< 2.5 mg m(-3)), data dispersion dominated in the retrievals with the MEGS (MERIS ground segment processor) processor. The lowest bias and data dispersion were obtained with MEGS for suspended particulate matter, for which overestimations in the range of 8-16% were found. Only the FUB retrieved CDOM (coloured dissolved organic matter) correlate with in situ values. However, a large systematic underestimation appears in the estimates that nevertheless may be corrected for by using a local correction factor. The MEGS has the potential to be used as an operational processing algorithm for the Himmerfjarden bay and adjacent areas, but it requires further improvement of the atmospheric correction for the blue bands and better definition at relatively low chlorophyll concentrations in the presence of high CDOM attenuation.

This study aims to highlight how satellite data can be used for an improved understanding of ecological processes in a narrow coastal bay. The usefulness of the Medium Resolution Imaging Spectrometer (MERIS) data (2003-2011) as a complement to the in situ monitoring in Himmerferdenn (HF) bay is used as an example that can also be applied to other coastal areas. HF bay is one of the most frequently monitored coastal areas in the world, allowing for a rigorous comparison between satellites and ship-based monitoring data. MERIS data was used for the integration of chlorophyll-a (chl-a) over each waterbody in the HF area, following the national waterbody classification by the Swedish Meteorological and Hydrological Institute (SMHI). Chl-a anomaly maps were produced for the bay and its adjacent areas. The maps could be used to show events with high chl-a, both with natural causes (e.g. a Prymnesium polylepis bloom observed in summer 2008) and of anthropogenic causes (e.g. failure in the local sewage treatment plant resulting in a strong spring bloom in 2006). Anomaly maps thereby allow to scan larger coastal stretches to discriminate areas that may require additional sampling by ship, or to identify areas that do not differ much from the median value of the MERIS time series.

An analysis of 11 years of sea surface temperatures images allowed the determination of the frontal occurrence probability in the southeastern Beaufort Sea using the single-image edge detection method. Results showed that, as the season progresses, fronts become more detectable due to solar heating of the surface layer. Some recurrent features can be identified in the summer time frontal climatology such as the Mackenzie River plume front, the Cape Bathurst front, the Mackenzie Trough front and the Amundsen Gulf front. These areas may be playing an important role in the biological processes acting as drivers to local enhanced biological productivity.

The Metalasia clade (Asteraceae–Gnaphalieae) consisting of the genera Metalasia, Atrichantha, Calotesta, Dolichothrix, Hydroidea, Lachnospermum, Phaenocoma, and Planea is endemic to South Africa with a main distribution within the Cape Floristic Region (CFR), a region known for its remarkable botanical diversity.

The monophyly of the Metalasia clade, the relationships of its genera, and the circumscription of these as well as their position within the tribe Gnaphalieae is investigated using molecular data. The study confirms the Metalasia clade to be a monophyletic group, untangling the relationships between the included genera.

Five new Metalasia species have been described since the latest revision of the genus, three of which are described in the present work. An updated key to all 57 species of the genus is also provided.

A phylogenetic study of the genus Metalasia, including all 57 species, based on a combination of morphological and molecular data shows that Metalasia consists of two sister clades, Clade A and Clade B, morphologically separated by the papillose cypselas of Clade A. Metalasia is, however, not supported as monophyletic, and Lachnospermum is placed together with the Metalasia species of Clade B. Further, the monotypic Planea, originally described as Metalasia schlechteri, is placed well within Clade B.

A biogeographical study reveals Metalasia to have evolved in the CFR around 6.9 Ma. Ancestral area estimations present a possible scenario for the radiation of Metalasia and show a difference between Clade A and B, correlated to the different rainfall regimes of southern Africa. The results show that Clade B began to diversify around 6.4 Ma in the winter rainfall area, whereas the diversification of the Clade A crown group, which is estimated to only 3.3 Ma, was initiated in the all-year rainfall area.

Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the Metalasia clade'. A species-level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA-trnH, trnL-trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well-supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M.densa which appears to be an intricate species complex.

Athroismeae is a small tribe of the Asteraceae-Asteroideae, the members of which show considerable variation in morphology. A molecular phylogenetic study of the tribe is presented for the first time, based on plastid (ndhF, trnH-psbA, trnL-trnF) and nuclear data (ETS, ITS). The phylogenetic relationships between the different genera within Athroismeae are discussed, and in addition, three unispecific genera: Anisochaeta, Artemisiopsis and Symphyllocarpus as well as Duhaldea (Inula) stuhlmannii, all earlier placed in other tribes, are here shown to belong within Athroismeae. Symphyllocarpus is sister to Centipeda and the earlier Symphyllocarpinae includes Centipedinae in synonymy. Furthermore, Cardosoa and Philyrophyllum are found to be integrated within Anisopappus and their generic status cannot be maintained. An outline of an amended circumscription of the Athroismeae is presented, with three new combinations and a description of the new subtribe Lowryanthinae.

AimThe Cape region is known for its exceptional species richness, although much remains unknown regarding the appearance of the modern Cape flora. One explanation is that floral diversification was influenced by the establishment of winter rainfall/summer arid conditions hypothesized to have occurred towards the end of the Miocene. We studied the evolution and diversification of the plant genus Metalasia (Asteraceae-Gnaphalieae), with the aim of testing whether radiation patterns may have been influenced by the climatic changes. LocationSouth Africa, with emphasis on the south-west. MethodsThe radiation of Metalasia was investigated using two approaches: a species diffusion approach, which estimated the ancestral areas by means of a relaxed random walk while sampling from extant distributions; and a discrete approach, in which distributions were defined according to the phytogeographical centres of the Cape region. Secondarily derived clock rates from an earlier Gnaphalieae study were used for calibration purposes. ResultsOur analyses date Metalasia to approximately 6.9Ma, after the Miocene-Pliocene boundary and the establishment of the winter rainfall/summer arid conditions. Metalasia consists of two sister clades: Clade A and Clade B. Clade B, which is endemic to the winter rainfall area, is estimated to have diversified c. 6.4Ma, whereas Clade A, with a main distribution in the all-year rainfall area, is considerably younger, with a crown group age estimated to 3.3Ma. Diversification rates suggest an early rapid speciation, with rates decreasing through time both for Metalasia and for clades A and B separately. Ancestral area estimations show a possible scenario for the radiation of Metalasia to its current diversity and distribution, with no conflict between results inferred from diffusion or discrete methods. Main conclusionsThe diversification of Metalasia is estimated to have begun after the establishment of the winter rainfall/summer arid conditions, consistent with its radiation having been influenced by changes in the climatic regime.